[chimerax-users] Silhouettes cause fill

[Ray Y.-R. Wang]

Hi Tom and Elaine,

Thanks for the answer. I had found a workaround on this issue and hope you
can help me understand this -- if I clip the plane using the buttons
(Clip/Clip rotate) available in "Right Mouse" panel and I don't see this
thick black edge anymore. Is it because the Clipping mode designated for
the buttons is for front and back clipping?

Obviously, the depthJump 0.1 solves the problem (thanks for the tip)!

Thanks!
Ray

On Mon, May 4, 2020 at 11:50 AM Tom Goddard <goddard at sonic.net> wrote:

> Hi Daniel,
>
>   It is the silhouette depth jump parameter that is causing this.  The
> default values is 0.03 and if you increase it
>
>         graphics silhouette depthJump 0.1
>
> that might solve your issue.  Let me explain what this parameter means.  A
> black silhouette edge is drawn at a pixel if a neighbor pixel differs in
> depth by 0.03 times the full depth of the scene (between near and far clip
> planes).  It is surprising to me that your helix has neighboring 2d pixels
> that differ in depth by more than 3% of the scene depth.  But the helix
> axis is almost aligned with the view direction so two adjacent pixels on
> the helix can be at quite different depths.  But also the full depth of
> your scene must be quite small, only a few times deeper than the length of
> the entire helix I guess.  Maybe there is a bug here.
>
>         Tom
>
> > On May 4, 2020, at 10:20 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Daniel,
> > Another parameter to play with is the graphics silhouettes "depthJump"
> value.  In this case you could try increasing it.  I've had similar
> problems, and at least part of the time, could solve them by fiddling with
> this value.
> >
> > <
> http://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
> >
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> >> On May 3, 2020, at 7:38 PM, Daniel Asarnow <asarnow at msg.ucsf.edu>
> wrote:
> >>
> >> Hi,
> >> Is there any way to avoid this effect where silhouettes lead to an
> apparent flood fill? The helix in the upper left of this clip shows what I
> mean:
> >> <image.png>
> >>
> >> I was able to work around it a bit by making the silhouettes thinner
> than I'd like, and aggressively supersampling. It seems severe with any
> silhouette width greater than 1.
> >>
> >> Thanks and best,
> >> -da
> >
> >
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